title: Development of dansyl-modified oligonucleotide probes responding to structural changes in a duplex.
abstract: We have synthesized a nonnucleoside amidite block of dansyl fluorophore to prepare dansyl-modified oligonucleotides (ONTs). The fluorescence intensities of dansyl-ONT specifically increased by the presence of adjacent guanosine residues but, significantly reduced in a dansyl-flipping duplex. These changes were caused by solvatochromism effect due to the number of guanine which is hydrophobic functional group and the external environment of dansyl group. The fluorescence intensities could be plotted as a function of the ONTs concentrations and the increase in the fluorescence was observed to equimolar concentrations of target DNA. This duplex exhibited higher melting temperature relative to the corresponding duplexes containing other base pairs. Similar changes in fluorescence could be detected upon hybridization with complementary RNAs. Thus, the dansyl-modified ONTs provide sequence specific fluorescent probe of DNA and RNA.
authors.affiliation: Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Keiko
authors.initials: K
authors.lastname: Kowata
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Komatsu
mesh_terms: D015374:Biosensing Techniques; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D005456:Fluorescent Dyes / Q000737:chemistry*; D015394:Molecular Structure; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry* / Q000235:genetics; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D010713:Phosphatidylcholines / Q000737:chemistry*; D011721:Pyrenes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013050:Spectrometry, Fluorescence / Q000379:methods; D013329:Structure-Activity Relationship
chemical_list: C496906:1-myristoyl-2-(12-((5-dimethylamino-1-naphthalenesulfonyl)amino)dodecanoyl)-sn-glycero-3-phosphocholine; D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D010713:Phosphatidylcholines; D011721:Pyrenes; D012313:RNA; D004247:DNA
keywords: DNA; Fluorescence; Molecular probes; RNA; Sensor